TY - JOUR AU - Cho, R. J. AU - Campbell, M. J. AU - Winzeler, E. A. AU - Steinmetz, L. AU - Conway, A. AU - Wodicka, L. AU - Wolfsberg, T. G. AU - Gabrielian, A. E. AU - Landsman, D. AU - Lockhart, D. J. PY - 1998 DA - 1998// TI - A genome-wide transcriptional analysis of the mitotic cell cycle JO - Molecular cell VL - 2 UR - https://doi.org/10.1016/S1097-2765(00)80114-8 DO - 10.1016/S1097-2765(00)80114-8 ID - Cho1998 ER - TY - JOUR AU - Laub, M. T. AU - McAdams, H. H. AU - Feldblyum, T. AU - Fraser, C. M. AU - Shapiro, L. PY - 2000 DA - 2000// TI - Global analysis of the genetic network controlling a bacterial cell cycle JO - Science (New York, NY) VL - 290 UR - https://doi.org/10.1126/science.290.5499.2144 DO - 10.1126/science.290.5499.2144 ID - Laub2000 ER - TY - JOUR AU - Menges, M. AU - Hennig, L. AU - Gruissem, W. AU - Murray, J. A. PY - 2002 DA - 2002// TI - Cell cycle-regulated gene expression in Arabidopsis JO - The Journal of biological chemistry VL - 277 UR - https://doi.org/10.1074/jbc.M207570200 DO - 10.1074/jbc.M207570200 ID - Menges2002 ER - TY - JOUR AU - Spellman, P. T. AU - Sherlock, G. AU - Zhang, M. Q. AU - Iyer, V. R. AU - Anders, K. AU - Eisen, M. B. AU - Brown, P. O. AU - Botstein, D. AU - Futcher, B. PY - 1998 DA - 1998// TI - Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization JO - Molecular biology of the cell VL - 9 UR - https://doi.org/10.1091/mbc.9.12.3273 DO - 10.1091/mbc.9.12.3273 ID - Spellman1998 ER - TY - JOUR AU - Whitfield, M. L. AU - Sherlock, G. AU - Saldanha, A. J. AU - Murray, J. I. AU - Ball, C. A. AU - Alexander, K. E. AU - Matese, J. C. AU - Perou, C. M. AU - Hurt, M. M. AU - Brown, P. O. PY - 2002 DA - 2002// TI - Identification of genes periodically expressed in the human cell cycle and their expression in tumors JO - Molecular biology of the cell VL - 13 UR - https://doi.org/10.1091/mbc.02-02-0030. DO - 10.1091/mbc.02-02-0030. ID - Whitfield2002 ER - TY - JOUR AU - de Lichtenberg, U. AU - Jensen, L. J. AU - Fausboll, A. AU - Jensen, T. S. AU - Bork, P. AU - Brunak, S. PY - 2005 DA - 2005// TI - Comparison of computational methods for the identification of cell cycle-regulated genes JO - Bioinformatics (Oxford, England) VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti093 DO - 10.1093/bioinformatics/bti093 ID - de Lichtenberg2005 ER - TY - JOUR AU - Rustici, G. AU - Mata, J. AU - Kivinen, K. AU - Lio, P. AU - Penkett, C. J. AU - Burns, G. AU - Hayles, J. AU - Brazma, A. AU - Nurse, P. AU - Bahler, J. PY - 2004 DA - 2004// TI - Periodic gene expression program of the fission yeast cell cycle JO - Nature genetics VL - 36 UR - https://doi.org/10.1038/ng1377 DO - 10.1038/ng1377 ID - Rustici2004 ER - TY - JOUR AU - Peng, X. AU - Karuturi, R. K. AU - Miller, L. D. AU - Lin, K. AU - Jia, Y. AU - Kondu, P. AU - Wang, L. AU - Wong, L. S. AU - Liu, E. T. AU - Balasubramanian, M. K. PY - 2005 DA - 2005// TI - Identification of cell cycle-regulated genes in fission yeast JO - Molecular biology of the cell VL - 16 UR - https://doi.org/10.1091/mbc.E04-04-0299 DO - 10.1091/mbc.E04-04-0299 ID - Peng2005 ER - TY - JOUR AU - Oliva, A. AU - Rosebrock, A. AU - Ferrezuelo, F. AU - Pyne, S. AU - Chen, H. AU - Skiena, S. AU - Futcher, B. AU - Leatherwood, J. PY - 2005 DA - 2005// TI - The cell cycle-regulated genes of Schizosaccharomyces pombe JO - PLoS biology VL - 3 UR - https://doi.org/10.1371/journal.pbio.0030225 DO - 10.1371/journal.pbio.0030225 ID - Oliva2005 ER - TY - CHAP AU - Pyne, S. AU - Futcher, B. AU - Skiena, S. PY - 2008 DA - 2008// TI - Meta-Analysis of Microarray Data BT - Bioinformatics Algorithms: Techniques and Applications PB - Wiley-Interscience; Hoboken, NJ CY - Mandoiu IaAZ ID - Pyne2008 ER - TY - JOUR AU - Marguerat, S. AU - Jensen, T. S. AU - de Lichtenberg, U. AU - Wilhelm, B. T. AU - Jensen, L. J. AU - Bahler, J. PY - 2006 DA - 2006// TI - The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast JO - Yeast (Chichester, England) VL - 23 UR - https://doi.org/10.1002/yea.1351 DO - 10.1002/yea.1351 ID - Marguerat2006 ER - TY - JOUR AU - Benjamini, Y. AU - Hochberg, Y. PY - 1995 DA - 1995// TI - Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing JO - Journal of the Royal Statistical Society Series B-Methodological VL - 57 ID - Benjamini1995 ER - TY - CHAP AU - Fisher, N. I. PY - 1996 DA - 1996// BT - Statistical Analysis of Circular Data PB - Cambridge University Press CY - New York ID - Fisher1996 ER - TY - CHAP AU - Kaufman, L. AU - Rousseeuw, P. J. PY - 2006 DA - 2006// BT - Finding Groups in Data: An Introduction to Cluster Analysis PB - Sons, Incorporated CY - Hoboken, NJ ID - Kaufman2006 ER - TY - JOUR AU - Rousseeuw, P. J. PY - 1987 DA - 1987// TI - Silhouettes - a Graphical Aid to the Interpretation and Validation of Cluster-Analysis JO - Journal of Computational and Applied Mathematics VL - 20 UR - https://doi.org/10.1016/0377-0427(87)90125-7 DO - 10.1016/0377-0427(87)90125-7 ID - Rousseeuw1987 ER - TY - JOUR AU - Kim, C. S. AU - Bae, C. S. AU - Tcha, H. J. PY - 2008 DA - 2008// TI - A phase synchronization clustering algorithm for identifying interesting groups of genes from cell cycle expression data JO - BMC bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-56 DO - 10.1186/1471-2105-9-56 ID - Kim2008 ER - TY - JOUR AU - Allefeld, C. AU - Kurths, J. PY - 2004 DA - 2004// TI - An approach to multivariate phase synchronization analysis and its application to event-related potentials JO - International Journal of Bifurcation and Chaos VL - 14 UR - https://doi.org/10.1142/S0218127404009521 DO - 10.1142/S0218127404009521 ID - Allefeld2004 ER - TY - CHAP AU - Liu, X. AU - Brutlag, D. L. AU - Liu, J. S. PY - 2001 DA - 2001// TI - BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes BT - Proceedings of the Pacific Symposium on Biocomputing ID - Liu2001 ER - TY - STD TI - Fu Y, Frith MC, Haverty PM, Weng Z: MotifViz: an analysis and visualization tool for motif discovery. Nucleic acids research. 2004, W420-423. 10.1093/nar/gkh426. 32 Web Server ID - ref19 ER - TY - JOUR AU - Wingender, E. AU - Chen, X. AU - Fricke, E. AU - Geffers, R. AU - Hehl, R. AU - Liebich, I. AU - Krull, M. AU - Matys, V. AU - Michael, H. AU - Ohnhauser, R. PY - 2001 DA - 2001// TI - The TRANSFAC system on gene expression regulation JO - Nucleic acids research VL - 29 UR - https://doi.org/10.1093/nar/29.1.281 DO - 10.1093/nar/29.1.281 ID - Wingender2001 ER - TY - STD TI - O'Brien KP, Remm M, Sonnhammer EL: Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic acids research. 2005, D476-480. 33 Database ID - ref21 ER - TY - STD TI - Penkett CJ, Morris JA, Wood V, Bahler J: YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. Nucleic acids research. 2006, W330-334. 10.1093/nar/gkl311. 34 Web Server ID - ref22 ER - TY - STD TI - Gauthier NP, Larsen ME, Wernersson R, de Lichtenberg U, Jensen LJ, Brunak S, Jensen TS: Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. Nucleic acids research. 2008, D854-859. 36 Database ID - ref23 ER - TY - JOUR AU - Lu, X. AU - Zhang, W. AU - Qin, Z. S. AU - Kwast, K. E. AU - Liu, J. S. PY - 2004 DA - 2004// TI - Statistical resynchronization and Bayesian detection of periodically expressed genes JO - Nucleic acids research VL - 32 UR - https://doi.org/10.1093/nar/gkh205 DO - 10.1093/nar/gkh205 ID - Lu2004 ER - TY - JOUR AU - Liu, D. AU - Umbach, D. M. AU - Peddada, S. D. AU - Li, L. AU - Crockett, P. W. AU - Weinberg, C. R. PY - 2004 DA - 2004// TI - A random-periods model for expression of cell-cycle genes JO - Proceedings of the National Academy of Sciences of the United States of America VL - 101 UR - https://doi.org/10.1073/pnas.0402285101 DO - 10.1073/pnas.0402285101 ID - Liu2004 ER - TY - JOUR AU - Caretta-Cartozo, C. AU - De Los Rios, P. AU - Piazza, F. AU - Lio, P. PY - 2007 DA - 2007// TI - Bottleneck genes and community structure in the cell cycle network of S. pombe JO - PLoS computational biology VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030103 DO - 10.1371/journal.pcbi.0030103 ID - Caretta-Cartozo2007 ER - TY - JOUR AU - Langmead, C. J. AU - Yan, A. K. AU - McClung, C. R. AU - Donald, B. R. PY - 2003 DA - 2003// TI - Phase-independent rhythmic analysis of genome-wide expression patterns JO - J Comput Biol VL - 10 UR - https://doi.org/10.1089/10665270360688165 DO - 10.1089/10665270360688165 ID - Langmead2003 ER - TY - JOUR AU - Tsiporkova, E. AU - Boeva, V. PY - 2008 DA - 2008// TI - Fusing time series expression data through hybrid aggregation and hierarchical merge JO - Bioinformatics (Oxford, England) VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn264 DO - 10.1093/bioinformatics/btn264 ID - Tsiporkova2008 ER - TY - CHAP AU - Rao, J. S. AU - Sengupta, A. PY - 2001 DA - 2001// BT - Topics in Circular Statistics PB - World Scientific Publishing Company CY - Singapore ID - Rao2001 ER - TY - JOUR AU - Zhang, N. AU - Gong, Z. Z. AU - Minden, M. AU - Lu, M. PY - 1993 DA - 1993// TI - The HOX-11 (TCL-3) homeobox proto-oncogene encodes a nuclear protein that undergoes cell cycle-dependent regulation JO - Oncogene VL - 8 ID - Zhang1993 ER - TY - JOUR AU - Kawabe, T. AU - Muslin, A. J. AU - Korsmeyer, S. J. PY - 1997 DA - 1997// TI - HOX11 interacts with protein phosphatases PP2A and PP1 and disrupts a G2/M cell-cycle checkpoint JO - Nature VL - 385 UR - https://doi.org/10.1038/385454a0 DO - 10.1038/385454a0 ID - Kawabe1997 ER - TY - JOUR AU - Futschik, M. E. AU - Herzel, H. PY - 2008 DA - 2008// TI - Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis JO - Bioinformatics (Oxford, England) VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn072 DO - 10.1093/bioinformatics/btn072 ID - Futschik2008 ER - TY - JOUR AU - Jensen, L. J. AU - de Lichtenberg, U. AU - Jensen, T. S. AU - Brunak, S. AU - Bork, P. PY - 2008 DA - 2008// TI - Circular reasoning rather than cyclic expression JO - Genome biology VL - 9 UR - https://doi.org/10.1186/gb-2008-9-6-403 DO - 10.1186/gb-2008-9-6-403 ID - Jensen2008 ER - TY - JOUR AU - Lu, Y. AU - Mahony, S. AU - Benos, P. V. AU - Rosenfeld, R. AU - Simon, I. AU - Breeden, L. L. AU - Bar-Joseph, Z. PY - 2007 DA - 2007// TI - Combined analysis reveals a core set of cycling genes JO - Genome biology VL - 8 UR - https://doi.org/10.1186/gb-2007-8-7-r146 DO - 10.1186/gb-2007-8-7-r146 ID - Lu2007 ER - TY - JOUR AU - Ptitsyn, A. A. AU - Zvonic, S. AU - Conrad, S. A. AU - Scott, L. K. AU - Mynatt, R. L. AU - Gimble, J. M. PY - 2006 DA - 2006// TI - Circadian clocks are resounding in peripheral tissues JO - PLoS computational biology VL - 2 UR - https://doi.org/10.1371/journal.pcbi.0020016 DO - 10.1371/journal.pcbi.0020016 ID - Ptitsyn2006 ER - TY - JOUR AU - Ptitsyn, A. A. AU - Zvonic, S. AU - Gimble, J. M. PY - 2006 DA - 2006// TI - Permutation test for periodicity in short time series data JO - BMC bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-S2-S10 DO - 10.1186/1471-2105-7-S2-S10 ID - Ptitsyn2006 ER - TY - JOUR AU - Ptitsyn, A. A. AU - Zvonic, S. AU - Gimble, J. M. PY - 2007 DA - 2007// TI - Digital signal processing reveals circadian baseline oscillation in majority of mammalian genes JO - PLoS computational biology VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030120 DO - 10.1371/journal.pcbi.0030120 ID - Ptitsyn2007 ER -